diff --git a/src/cook/cook_build.rs b/src/cook/cook_build.rs
index 2157dc2198..f68d4f2670 100644
--- a/src/cook/cook_build.rs
+++ b/src/cook/cook_build.rs
@@ -987,7 +987,22 @@ pub fn build(
             // vendored tree look untracked, so staging silently never fired and
             // builds kept mutating the git-tracked source.
             let source_real = source_dir.canonicalize().unwrap_or_else(|_| source_dir.to_path_buf());
-            let source_is_tracked = std::env::var_os("REDBEAR_IN_TREE_BUILD").is_none()
+
+            // Never stage a SUBMODULE. `git ls-files --error-unmatch` succeeds
+            // on a submodule's gitlink, so relibc & co. looked like ordinary
+            // tracked trees and got copied wholesale -- which broke their cargo
+            // builds (crt0/crti/crtn/ld_so all failed) because the nested repo
+            // context did not survive the copy.
+            //
+            // Skipping them is principled, not a workaround: each fork
+            // submodule is already covered by the stricter REFUSING-TO-BUILD
+            // dirty gate, which forbids uncommitted edits outright. Vendored
+            // recipe `source/` trees have no such guarantee, and they are the
+            // ones recipes actually rewrite.
+            let source_is_submodule = source_real.join(".git").exists();
+
+            let source_is_tracked = !source_is_submodule
+                && std::env::var_os("REDBEAR_IN_TREE_BUILD").is_none()
                 && Command::new("git")
                     .arg("ls-files")
                     .arg("--error-unmatch")
@@ -1000,17 +1015,38 @@ pub fn build(
 
             let effective_source = if source_is_tracked {
                 let staged = get_sub_target_dir(target_dir, "source-staged");
-                let _ = fs::remove_dir_all(&staged);
-                let status = Command::new("cp")
+
+                // Refresh IN PLACE; never remove the directory first.
+                //
+                // Qt bakes its COOKBOOK_SOURCE path into installed cmake files
+                // (QtSeparateDebugInfo.cmake try_compile()s against
+                // ${QT_SOURCE_TREE}/config.tests/...). Once that path is the
+                // staged tree, a `rm -rf` at the start of a rebuild makes it
+                // vanish underneath consumers that are configuring against it:
+                //   CMake Error: The source ".../qtbase/.../source-staged/
+                //     config.tests/binary_for_strip/CMakeLists.txt" does not ...
+                // (qtsvg and qtshadertools, both mid-configure).
+                //
+                // rsync --delete gives the same pristine result -- files the
+                // last build's seds added are removed, modified ones are
+                // restored from the tracked tree -- while the directory itself
+                // continues to exist throughout.
+                let _ = fs::create_dir_all(&staged);
+                let mut src_slash = source_real.clone().into_os_string();
+                src_slash.push("/");
+                let mut dst_slash = staged.clone().into_os_string();
+                dst_slash.push("/");
+                let status = Command::new("rsync")
                     .arg("-a")
-                    .arg("--reflink=auto")
-                    .arg(&source_real)
+                    .arg("--delete")
+                    .arg(src_slash)
+                    .arg(dst_slash)
                     .arg(&staged)
                     .status()
                     .map_err(|e| format!("failed to stage source out of tree: {e}"))?;
                 if !status.success() {
                     return Err(format!(
-                        "failed to stage source out of tree: cp exited {status}"
+                        "failed to stage source out of tree: rsync exited {status}"
                     ));
                 }
                 log_to_pty!(